A 2/3-approximation algorithm for vertex-weighted matching
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AMG Preconditioners based on parallel hybrid coarsening and multi-objective graph matching
We describe preliminary results from a multi-objective graph matching algorithm, in the coarsening step of an aggregation-based Algebraic MultiGrid (AMG) preconditioner, for solving large and sparse linear systems of equations on high-end parallel computers. We have two objectives. First, we wish to improve the convergence behavior of the AMG method when applied to highly anisotropic problems. Second, we wish to extend the parallel package \texttt{PSCToolkit} to exploit multi-threaded parallelism at the node level on multi-core processors. Our matching proposal balances the need to simultaneously compute high weights and large cardinalities by a new formulation of the weighted matching problem combining both these objectives using a parameter $\lambda$. We compute the matching by a parallel $2/3-\varepsilon$-approximation algorithm for maximum weight matchings. Results with the new matching algorithm show that for a suitable choice of the parameter $\lambda$ we compute effective preconditioners in the presence of anisotropy, i.e., smaller solve times, setup times, iterations counts, and operator complexity.
D'Ambra, Pasqua↗
Reduction-oxidation state and protein degradation in skeletal muscle of fasted and refed rats
Redox state and protein degradation were measured in isolated muscles of fasted (up to 10 d) and refed (up to 4 d) 7- to 14-wk-old rats. Protein degradation in the extensor digitorum longus muscle, but not in the soleus muscle, was greater in the fasted rats than in weight-matched muscle from fed rats. The NAD couple was more oxidized in incubated and fresh extensor digitorum longus muscles and in some incubated soleus muscles of fasted rats than in weight-matched muscle from fed rats. In the extensor digitorum longus muscle of refed or prolonged fasted rats, protein degradation was slower and the NAD couple was more reduced than in the fed state. Therefore, oxidation of the NAD couple was associated with increased muscle breakdown during fasting, whereas reduction of the NAD couple was associated with muscle conservation and deposition.
Fagan, Julie M.↗
cuAlign: Scalable Network Alignment on GPU Accelerators
Given two graphs, the objective of network alignment is to find the best one-to-one mapping of vertices in one graph (??) to vertices in the other (??), such that the number of overlaps is maximized. We say that edges(??, ??) ???and(??', ??') ??? are overlapped if ?? is mapped to ??' and ?? is mapped to??'. Network alignment is an important optimization problem with several applications in bioinformatics, computer vision and ontology matching. Since it is an NP-hard problem, efficient heuristics and scalable implementations are necessary. In this work, we introduce a new framework that combines the concepts of intra-network proximity using vertex embedding,Belief Propagation (BP) and approximate weighted matching, and provides qualitative improvements up to22%over state-of-the-art approaches. We also provide scalable implementations on GPU accelerators, demonstrating up to19×speedup for Belief Propagation and 3× speedup for approximate weighted matching relative to previous multithreaded implementation. A combination of combinatorial and algebraic kernels within the network alignment algorithm poses significant hurdles for parallelization. Load imbalance and irregular DRAM traffic limit achievable performance on GPUs. Our novel approach identifies and exploits unique structural proper-ties of the BP-based algorithm and employs code fusion to reduce data movement between different steps of the algorithm. Using a diverse set of inputs, we demonstrate qualitative improvements of our algorithms, and performance gains of our GPU-accelerated implementation. We believe that our work will enable algorithmic improvements and practical applications of network alignment.
Xiang, Lizhi↗
Streaming Matching and Edge Cover in Practice
Graph algorithms with polynomial space and time requirements often become infeasible for massive graphs with billions of edges or more. State-of-the-art approaches therefore employ approximate serial, parallel, and distributed algorithms to tackle these challenges. However, such approaches require storing the entire graph in memory and thus need access to costly computing resources such as clusters and supercomputers. In this paper, we present practical streaming approaches for solving massive graph problems using limited memory for two prototypical graph problems: maximum weighted matching and minimum weighted edge cover. For matching, we conduct a thorough computational study on two of the semi-streaming algorithms including a recent breakthrough result that achieves a $1/(2+\varepsilon)$-approximation of the weight while using $O( n \log W /\epsilon)$ memory (here $n$ is the number of vertices and $W$ is the maximum edge weight), designed by Paz and Schwartzman [SODA, 2017]. Empirically, we show that the semi-streaming algorithms produce matchings whose weight is close to the best $1/2$-approximate offline algorithm while requiring less time and an order-of-magnitude less memory. For minimum weighted edge cover, we develop three novel semi-streaming algorithms. Two of these algorithms require a single pass through the input graph, require $O(n \log n)$ memory, and provide a 2-approximation guarantee on the objective. We also leverage a relationship between approximate maximum weighted matching and approximate minimum weighted edge cover to develop a two-pass $3/2+\epsilon$-approximate algorithm with the memory requirement of Paz and Schwartzman's semi-streaming matching algorithm. These streaming approaches are compared against the state-of-the-art 3/2-approximate offline algorithm. The semi-streaming matching and the novel edge cover algorithms proposed in this paper can process graphs with several billions of edges in under 30 minutes using 6 GB of memory, which is at least an order of magnitude improvement from the offline (non-streaming) algorithms. For the largest graph, the best alternative offline parallel approximation algorithm (GPA+ROMA) could not finish in three hours even while employing hundreds of processors and 1 TB of memory. We also demonstrate an application of the semi-streaming algorithm by computing a matching using linearly bounded memory on item intersection graphs derived from three machine learning datasets, whereas the existing offline algorithms could not complete on one of these datasets since their memory requirements exceeded 1TB.
Ferdous, S M.↗
Flexible Weighting-And-Matching Scheme For Incomplete Data
Method for partial matching of data makes conventional electronic memory addressable via its contents. When implemented by suitable algorithm, method enables computer system containing memory to search memory for datum making exact or best approximate match to datum in query. Advantages are: requires neither long "learning" time nor "retraining" when additional data stored and attaches to each datum relative importance that can change with time without decreasing speed of retrieval. Responses include exact or approximate recollection, indications of ambiguity, avoidance, and even forgetfulness.
Wang, Lui↗
Optical processing for landmark identification
A study of optical pattern recognition techniques, available components and airborne optical systems for use in landmark identification was conducted. A data base of imagery exhibiting multisensor, seasonal, snow and fog cover, exposure, and other differences was assembled. These were successfully processed in a scaling optical correlator using weighted matched spatial filter synthesis. Distinctive data classes were defined and a description of the data (with considerable input information and content information) emerged from this study. It has considerable merit with regard to the preprocessing needed and the image difference categories advanced. A optical pattern recognition airborne applications was developed, assembled and demontrated. It employed a laser diode light source and holographic optical elements in a new lensless matched spatial filter architecture with greatly reduced size and weight, as well as component positioning toleranced.
Casasent, D.↗
Dynamic compensatory pattern matching in a fuzzy rule-based control system
A dynamic compensatory matching procedure is suggested as a method to generate an aggregated measure for evaluating the appropriateness of rules for control systems. It is a dynamic weighted matching technique which takes into account incomplete information under real-time requirements. The initial weights of importance of variables are generated with a generalized neural network architecture and a gradient descent algorithm. An intuitive compensatory scheme based on correlations among input variables of training data is adopted so that the system is coherent to a noisy environment.
Sun, Chuen-Tsai↗
Maturation of bone and dentin matrices in rats flown on the Soviet biosatellite Cosmos 1887
We have studied the chemistry, hydroxyapatite crystal size, and maturational changes in bone and dentin from rats exposed to microgravity for 12 days in a Soviet biosatellite (Cosmos 1887). Bone ash was reduced in vertebrae (L5) but not in the non-weight-bearing calvaria or mandibles. All tissues had a relatively normal percentage composition of Ca, P, and Mg. Nevertheless, flight rat calvaria and vertebral tissues tended to exhibit lower Ca/P and higher Ca/Mg ratios that any of their weight-matched controls groups, and gradient density analysis (calvaria) indicated a strong shift to the fractions lower specific gravity that was commensurate with impaired rates of matrix-mineral maturation. X-ray diffraction data were confirmatory. Bone hydroxyapatite crystal growth in the mandibles of flight rats was preferentially altered in such a way as to reduce their size (C-axis dimension). But in the mandibular diastemal region devoid of muscle attachments, flight rat bone and dentin were normal with respect to the Ca, P, Mg, and Zn concentrations and Ca/P and Ca/Mg ratios of age-matched controls. These observations affirm the concept that while microgravity most adversely affects the maturation of newly formed matrix and mineral moieties in weight-bearing bone, such effects occur throughout the skeleton.
NASA Experiment Number COS 1887-33↗
Enhanced skeletal muscle insulin sensitivity in year-old rats adapted to hypergravity
Rats induced into a hypermetabolic state by exposure to chronic (7 mo) centrifugation at 4.15 g exhibited increased glucose uptake at lower plasma insulin levels than weight-matched control animals following oral glucose administration. In order to determine the insulin sensitivity of specific tissues, the effect of exogenous insulin on glucose uptake by isolated perfused livers and hindlim skeletal muscle from rats adapted to chronic centrifugation for one year was compared with perfused tissue from 2.5 mo-old noncentrifuged control animals of equal body weight. Metabolic glucose clearance by skeletal muscle from hypergravic rats did not prove significantly greater than control muscle when perfused in the absence of insulin (10.6 vs 8.1 microliters/min-g-muscle), but was twice as fast (23.0 vs 9.5) at perfusate insulin levels of 35 micro-U/ml. Conversely, glucose uptake by hypergravic livers was significantly decreased (P is less than 0.001) compared with control livers (10.3 vs 27.8) at perfusate insulin levels of 40 micro-U/ml. Results suggest that skeletal muscle rather than liver is primarily responsible for the enhanced sensitivity to insulin and the increased energy expenditure observed in rats subjected to hypergravity.
Mondon, C. E.↗
Time course changes in [Ca2+]i, force, and protein content in hindlimb-suspended mouse soleus muscles
BACKGROUND: Exposure to reduced gravitational forces during spaceflight is associated with significant reductions in skeletal muscle mass and strength. The purpose of this study was to test the hypothesis that increases in resting cytosolic free calcium concentration ([Ca2+]i) would precede reductions in protein content and maximal isometric tetanic force (Po) in mouse soleus muscle after initiation of hindlimb suspension. METHODS: Female ICR mice (n = 42) were hindlimb suspended for 1, 2, 3, 5, or 7 d; weight-matched mice were used as controls. Following the hindlimb suspension, the left soleus muscle was used to determine Po in vitro and the right soleus muscle was used to determine protein content and [Ca2+]i via confocal laser scanning microscopy. RESULTS: Compared with controls, [Ca2+]i was elevated by 38% at 2 d, and 117% at 7 d. Compared with controls, soleus muscle total and myofibrillar protein contents were reduced 27-29% and 30-34%, respectively, at 5-7 d after initiation of hindlimb suspension. Compared with controls, soleus muscle Po was decreased by 24% at 3 d, and 38% at 7 d. CONCLUSION: It appears that resting cytosolic Ca2+ homeostasis is disturbed soon after the initiation of hindlimb suspension, and these elevations in [Ca2+]i may play a role in initiating soleus muscle atrophy.
Non-NASA Center↗
Pan‐Cancer Survival Impact of Immune Checkpoint Inhibitors in a National Healthcare System
ABSTRACT Background The cumulative, health system‐wide survival benefit of immune checkpoint inhibitors (ICIs) is unclear, particularly among real‐world patients with limited life expectancies and among subgroups poorly represented on clinical trials. We sought to determine the health system‐wide survival impact of ICIs. Methods We identified all patients receiving PD‐1/PD‐L1 or CTLA‐4 inhibitors from 2010 to 2023 in the national Veterans Health Administration (VHA) system (ICI cohort) and all patients who received non‐ICI systemic therapy in the years before ICI approval (historical control). ICI and historical control cohorts were matched on multiple cancer‐related prognostic factors, comorbidities, and demographics. The effect of ICI on overall survival was quantified with Cox regression incorporating matching weights. Cumulative life‐years gained system‐wide were calculated from the difference in adjusted 5‐year restricted mean survival times. Results There were 27,322 patients in the ICI cohort and 69,801 patients in the historical control cohort. Among ICI patients, the most common cancer types were NSCLC (46%) and melanoma (10%). ICI demonstrated a large OS benefit in most cancer types with heterogeneity across cancer types (NSCLC: adjusted HR [aHR] 0.56, 95% confidence interval [CI] 0.54–0.58,p < 0.001; urothelial: aHR 0.91, 95% CI 0.83–1.01,p = 0.066). The relative benefit of ICI was stable across patient age, comorbidity, and self‐reported race subgroups. Across VHA, 15,859 life‐years gained were attributable to ICI within 5‐years of treatment, with NSCLC contributing the most life‐years gained. Conclusion We demonstrated substantial increase in survival due to ICIs across a national health system, including in patient subgroups poorly represented on clinical trials.
Oncology↗
ECP-ExaGraph/netAlign
We investigate substituting a parallel, half-approximation for maximum weight matching instead of an exact computation. Our experiments show that the resulting difference in solution quality is negligible. We demonstrate almost a 20-fold speedup using 40 threads on an 8 processor Intel Xeon E7-8870 system and now solve real-world problems in 36 seconds instead of 10 minutes
Khan, Arif↗
Exercise, dietary obesity, and growth in the rat
Experiments were conducted on weanling male rats 35 days old and weighing about 100 g to determine how endurance-type exercise and high-fat diet administered during growth influence body mass and composition. The animals were divided into four weight-matched groups of 25 animals each: group I - high-fat diet, exercised; group II - chow, exercised; group III - high-fat diet, sedentary; and group IV - chow, sedentary. During growth, masses of water, muscle and skin increased as functions of body size; bone as a function of age; and heart, liver, gut, testes, and CNS were affected by combinations of size, age, activity, and diet. Major conclusions are that growth in body size is expressed more precisely with fat-free body mass (FFBM), that late rectilinear growth is probably attributable to fat accretion, and that the observed influences on FFBM of exercise and high-fat diet are obtained only if the regimen is started at or before age 5-7 weeks.
Pitts, G. C.↗
Implications of otoconial changes in microgravity
Otoconia of maculas of Sprague-Dawley rats (Taconic Farms) flown aboard Spacelab-3 showed no signs of demineralization. Other findings were accumulations of miniature otoconia at the lateral border of utricular patches and a smoothing of surfaces of saccular otoconia. These features were not observed in age- and weight-matched ground controls. Subsequent study showed otoconial asymmetry to be normal in this strain. Further research in space, taking this into account, is clearly required. Findings of ground-based studies would suggest that neural structures of maculas are adaptable to microgravity but might show changes over time. Moreover, maculas have the potential for integration of the sort ascribed to brain and retina, although on a less complex scale. They may act as comparators, and asymmetry may be an important property. Coordinated studies in space and on the ground could lead to new understanding of how maculas function and adapt to new acceleratory environments; and to insights about the functioning of neural tissue in general.
Ross, Muriel D.↗
Monolithic and mechanical multijunction space solar cells
Monolithic and mechanically stacked tandem solar cells have been fabricated with encouraging AM0 efficiencies summarized as: monolithic GaAs/Ge: 19.1 percent (28 C, 4 sq cm); monolithic InP/Ga0.47In0.53As: 22.2 percent (25 C, 0.296 sq cm); monolithic AlGaAs/GaAs/InGaAs: 27.6 percent (80 C, 0.2 sq cm, 100 X); mechanically stacked GaAs/GaSb: 30.8 percent (25 C, 0.049 sq cm, 100 X); and mechanically stacked GaAs/CuInSe2: 23.1 percent (25 C, 4 sq cm). Significant improvement in tandem cell efficiencies nearing to theoretical predictions has been projected with the improvement in cell material quality and processing. Thin-film cells offer improved specific power. It is pointed out that both the monolithic and mechanically stacked cells have their own problems as to size, processing, current-voltage matching, weight, etc. More information is needed on the effect of temperature and radiation on the cell performance. Proper reference cells and full spectrum range simulators are required to measure efficiencies correctly.
Jain, Raj K.↗
Monolithic and mechanical multijunction space solar cells
High-efficiency, lightweight, radiation-resistant solar cells are essential to meet the large power requirements of future space missions. Single-junction cells are limited in efficiency. Higher cell efficiencies could be realized by developing multijunction, multibandgap solar cells. Monolithic and mechanically stacked tandem solar cells surpassing single-junction cell efficiencies have been fabricated. This article surveys the current status of monolithic and mechanically stacked multibandgap space solar cells, and outlines problems yet to be resolved. The monolithic and mechanically stacked cells each have their own problems related to size, processing, current and voltage matching, weight, and other factors. More information is needed on the effect of temperature and radiation on the cell performance. Proper reference cells and full-spectrum range simulators are also needed to measure efficiencies correctly. Cost issues are not addressed, since the two approaches are still in the developmental stage.
Jain, Raj K.↗
Effect of insulin-like factors on glucose transport activity in unweighted rat skeletal muscle
The effect of 3 or 6 days of unweighting on glucose transport activity, as assessed by 2-deoxyglucose uptake, in soleus strips stimulated by maximally effective concentrations of insulin, IGF-I, vanadate, or phospholipase C (PLC) is examined. Progressively increased responses to maximally effective doses of insulin or insulin-like growth factor were observed after 3 and 6 days of unweighting compared with weight matched control strips. Enhanced maximal responses to vanadate (6 days only) and PLC (3 and 6 days) were also observed. The data provide support for the existance of postreceptor binding mechanisms for the increased action of insulin on the glucose transport system in unweighted rat skeletal muscle.
Henriksen, Erik J.↗